Little is known about the coordination relationship between Ministries of Health and other sectors to advance health and development goals in low- and middle-income countries (LMICs). Our study examined the coordination relationship between MoH and other government ministries, departments and agencies (MDAs) at the national level in Uganda. Document review and key informant interviews with government officials and non-state actors indicated the coordination relationship was characterized by interdependencies generally framed in terms of health sector goals and not vice versa. Actor opportunism and asymmetrical interests interacted with structural–institutional factors contributing to variable influence on internal and external coordination within and beyond MOH. The study suggests critical actions needed to improve coordination.